Biomechanics, one molecule at a time

Single-Molecule Mechanics in Ligand Concentration Gradient

Single-molecule experiments provide unique insights into the mechanisms of biomolecular phenomena. However, because varying the concentration of a solute usually requires the exchange of the entire solution around the molecule, ligand-concentration-dependent measurements on the same molecule pose a challenge. In the present work we exploited the fact that a diffusion-dependent concentration gradient arises in a laminar-flow microfluidic device, which may be utilized for controlling the concentration of the ligand that the mechanically manipulated single molecule is exposed to. We tested this experimental approach by exposing a λ-phage dsDNA molecule, held with a double-trap optical tweezers instrument, to diffusionally-controlled concentrations of SYTOX Orange (SxO) and tetrakis(4-N-methyl)pyridyl-porphyrin (TMPYP). We demonstrate that the experimental design allows access to transient-kinetic, equilibrium and ligand-concentration-dependent mechanical experiments on the very same single molecule.

SERS detection of microRNA biomarkers for cancer diagnosis using gold-coated paramagnetic nanoparticles to capture SERS-active gold nanoparticles

A highly sensitive magnetic-capture SERS assay for detecting cancer-related microRNAs was developed by enhancing the formation of SERS “hot spots”.

Surface-enhanced resonance Raman scattering (SERRS) simulates PCR for sensitive DNA detection

This paper describes a novel double-stranded DNA detection method through resonance between SYBR Green I and DNA with the surface-enhanced resonance Raman scattering (SERRS) assay, which opens an avenue to the quantitative and reliable application of SERRS in DNA detection.

Fe₃O₄@Ag magnetic nanoparticles for microRNA capture and duplex-specific nuclease signal amplification based SERS detection in cancer cells

A functionalized Fe3O4@Ag magnetic nanoparticle (NP) biosensor for microRNA (miRNA) capture and ultrasensitive detection in total RNA extract from cancer cells was reported in this paper. Herein, Raman tags-DNA probes modified Fe3O4@Ag NPs were designed both as surface-enhanced Raman scattering (SERS) SERS and duplex-specific nuclease signal amplification (DSNSA) platform. Firstly, target miRNAs were captured to the surface of Fe3O4@Ag NPs through DNA/RNA hybridization. In the presence of endonuclease duplex specific nuclease (DSN), one target miRNA molecule could rehybrid thousands of DNA probes to trigger the signal-amplifying recycling. Base on the superparamagnetic of Fe3O4@Ag NPs, target miRNA let-7b can be captured, concentrated and direct quantified within a PE tube without any PCR preamplification treatment. The detection limit was 0.3fM (15 zeptomole, 50μL), nearly 3 orders of magnitude lower than conventional fluorescence based DSN biosensors for miRNA(∼100fM), even single-base difference between the let-7 family members can be discriminated. The result provides a novel proposal to combine the perfect single-base recognition and signal-amplifying ability of the endonuclease DSN with cost-effective SERS strategy for miRNA point-of-care (POC) clinical diagnostics.

Surface-enhanced Raman scattering detection of DNAs derived from virus genomes using Au-coated paramagnetic nanoparticles

A magnetic capture-based, surface-enhanced Raman scattering (SERS) assay for DNA detection has been developed which utilizes Au-coated paramagnetic nanoparticles (Au@PMPs) as both a SERS substrate and effective bioseparation reagent for the selective removal of target DNAs from solution. Hybridization reactions contained two target DNAs, sequence complementary reporter probes conjugated with spectrally distinct Raman dyes distinct for each target, and Au@PMPs conjugated with sequence complementary capture probes. In this case, target DNAs were derived from the RNA genomes of the Rift Valley Fever virus (RVFV) or West Nile virus (WNV). The hybridization reactions were incubated for a short period and then concentrated within the focus beam of an interrogating laser by magnetic pull-down. The attendant SERS response of each individually captured DNA provided a limit of detection sensitivity in the range 20-100 nM. X-ray diffraction and UV-vis analysis validated both the desired surface plasmon resonance properties and bimetallic composition of synthesized Au@PMPs, and UV-vis spectroscopy confirmed conjugation of the Raman dye compounds malachite green (MG) and erythrosin B (EB) with the RVFV and WNV reporter probes, respectively. Finally, hybridization reactions assembled for multiplexed detection of both targets yielded mixed MG/EB spectra and clearly differentiated peaks which facilitate the quantitative detection of each DNA target. On the basis of the simple design of a single-particle DNA detection assay, the opportunity is provided to develop magnetic capture-based SERS assays that are easily assembled and adapted for high-level multiplex detection using low-cost Raman instrumentation.

Single-molecule force spectroscopy of polycystic kidney disease proteins

Atomic force microscopy in its single-molecule force spectroscopy mode is a nanomanipulation technique that is extensively used for the study of the mechanical properties of proteins. It is particularly suited to examine their response to stretching (i.e., molecular elasticity and mechanical stability). Here, we describe protein engineering strategies and single-molecule AFM techniques for probing protein mechanics, with special emphasis on polycystic kidney disease (PKD) proteins. We also provide step-by-step protocols for preparing proteins and performing single-molecule force measurements.

Optical traps to study properties of molecular motors

In vitro motility assays enabled the analysis of coupling between ATP hydrolysis and movement of myosin along actin filaments or kinesin along microtubules. Single-molecule assays using laser trapping have been used to obtain more detailed information about kinesins, myosins, and processive DNA enzymes. The combination of in vitro motility assays with laser-trap measurements has revealed detailed dynamic structural changes associated with the ATPase cycle. This article describes the use of optical traps to study processive and nonprocessive molecular motor proteins, focusing on the design of the instrument and the assays to characterize motility.

High-resolution dual-trap optical tweezers with differential detection: an introduction

Optical traps or "optical tweezers" have become an indispensable tool in understanding fundamental biological processes. The ability to manipulate and probe individual molecules or molecular complexes has led to a new, more refined understanding of the mechanical properties of the fundamental building blocks of the cell, and of the mechanism by which molecular machines function. The field has seen a steady stream of technological advances that have greatly refined the technique. One major effort has been in developing methods to resolve motions at the angstrom level--the fundamental length scale for many biological processes. This drive has only recently come to fruition with the advent of high-resolution optical trapping techniques that can now detect movements on the scale of a single base pair of DNA, 3.4 A. Here we briefly review the basic concepts and components of optical traps and the single-molecule experiments in which they are used.

Plasmon-enhanced fluorescence from single fluorophores end-linked to gold nanorods

We reported a method to fabricate fluorescent probes preferentially end-linked to Au nanorods. In comparison with organic dyes, the single nanocomplexes provide significant improvement in signal brightness. The bioconjugated nanoantenna structure implicates an approach that is more convenient and amenable to integration for photonic, optoelectronic, and biotechnological applications.

Highly efficient detection of single fluorophores in blood serum samples with high autofluorescence

Single molecule detection (SMD) is usually performed on surface-immobilized molecules with diffraction-limited observation volumes, typically with confocal optics to suppress background from the sample and instrument. In this paper we consider the more difficult task of detecting single fluorophores in the presence of a substantial fluorescence background. We determined that for a readily accessible macroscopic observation volume of 1 pL that the background from undiluted blood serum was approximately equal to 2700 Cy5 molecules, and the background from whole blood equal to about 14 000 Cy5 molecules in whole blood. These high backgrounds appear to preclude the possibility of SMD of Cy5 molecules. However, we show that the signal-to-noise ratio (SNR) in high background samples can be increased dramatically by reduction of the observed volume. We were able to detect single surface-bound Cy5-labeled DNA (Cy5-DNA) oligomers in diluted blood serum with an SNR near 40. We also examined freely diffusing Cy5-DNA in blood serum. The data showed that single Cy5-DNA molecules could be detected even in the undiluted serum. We further investigated the SNR on silver island films. We found that the fluorescence signal was greatly enhanced in the presence of metallic nanostructures showing a larger SNR in the application tested. These results suggest the possibility of clinical assays based on SMD in blood serum and possibly whole blood. Increased SNR near metallic nanostructure could probably overcome the need for diffraction-limited volumes and enhance our ability to do in situ SMD.

Visualizing and manipulating individual protein molecules

Single-molecule imaging and manipulation techniques have evolved in the past decade from mere jaw-dropping attractions to essential laboratory tools. By applying single-molecule methods important insights otherwise unavailable have been obtained on various biomolecular systems. Constantly improving single-molecule imaging techniques keep expanding the scale of the explorable spatial detail, thereby providing possible solutions to getting around the debilitating diffraction limit present in physiological-condition structural investigations. In some areas, such as motor protein studies, single-molecule methods have become part of the routine and essential research toolkit. Entire research fields, such as single-molecule force spectroscopy, have been born. In the present review single-molecule visualization and manipulation methods are reviewed with a focus on proteins. Relevant signals and prominent applications are discussed along with experimental examples and recent important results. Finally, the perspectives of the single-molecule field are explored.

Self-organisation and orderly processes by individual protein complexes in the bacterial cell

In the bacterial cell, individual multimeric proteins and multiprotein assemblies perform and control orderly processes. Individual motor enzyme complexes accomplish highly complex functions, such as nucleic acid and protein syntheses, with impressive efficiency and fidelity. Lac operon repression by the lac repressor is effectively controlled via a single molecular switch. There are only few copies of, for example, DNA polymerase holoenzyme and lac repressor and few specific target molecules/sites, with which these protein complexes interact, present in a single E. coli cell. These interactive processes take place in submicron-sized spaces characterised by extreme crowding (volume exclusion) of macromolecules and small molecules, heterogeneity and non-ideality. Recent evidence reinforces the fundamental difference of the cytoplasmic as compared with in vitro ("test tube") reaction conditions. This is reflected in the breakdown of the applicability of "bulk phase" thermodynamic, macroscopic chemical kinetic and diffusion laws to interactions of individual macromolecules and target sites in a single cell. Stochastic kinetic models and stochastic simulations enable the statistical description and analysis of biochemical reactions and binding processes which involve small numbers of reactants. New unifying concepts and models are required for the quantitative understanding of the microscopic self-organisation of multi-protein complexes and the dynamic order at the single-protein assembly and single-switch level in the living cell.

Grabbing the cat by the tail: manipulating molecules one by one

Methods for manipulating single molecules are yielding new information about both the forces that hold biomolecules together and the mechanics of molecular motors. We describe here the physical principles behind these methods, and discuss their capabilities and current limitations.